Description

Sample type: SRA

Source name: bone marrow derivedOrganism: Mus musculusCharacteristics strain: C57BL/6Sex: maleage: 8 to 10 weeksGrowth protocol: After 1 day in 0.6ng/ml CSF1 in alpha+ MEM /15% FCS, non-adherent cells were incubated for a second day in a fresh dish containing 0.6ng/ml CSF1 in alpha+ MEM /15% FCS. Cells were then incubated for a further 4 days in alpha+ MEM /10% FCS containing 12ng/ml CSF1.Extracted molecule total RNAExtraction protocol: mRNA was harvested using RNeasy kit( QIAGEN) with DNase treatment on column. 1 ug of total RNA was used for the construction of sequencing libraries.RNA libraries were prepared for sequencing using standard Ion Torrent protocols

Description: C2_R1C1_C2_C3_allprobes_reads.txtC1_C2_C3_allprobes_log2_RPM.txtData processing: Torrent Suite Software 5.10 used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence- returning a fastq file (raw data)Reads were then mapped to the GRCm38.p6 genome using the open source Hisat2-2.0.5 aligner.The Hisat2 generated BAM files were uploaded into SeqMonk (version 1.42) with minimum mapping quality set to 60The edgeR platform, within SequeMonk, was uesed to generate lists of differential gene expression from the raw reads as is required in analysis of negative binomial distributionsTab-delimited text files of all genes and differentially expressed genes (at p<0.05, p<0.01 and p<0.001) showing raw reads or log2 RPM were output (processed files)AmpliseqTorrent Suite Software 5.10 used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Returning a fastq file (raw data) of reads associated with each of the 16000 barcoded primer pairs.Reads were then mapped to the GRCm38.p6 genome using the open source Hisat2-2.0.5 aligner.The Hisat2 generated BAM files were uploaded into SeqMonk (version 1.42) with minimum mapping quality set to 60The edgeR platform, within SequeMonk, was uesed to generate lists of differential gene expression from the raw reads as is required in analysis of negative binomial distributionsTab-delimited text files of all genes and differentially expressed genes (at p<0.05, p<0.01 and p<0.001) showing raw reads or log2 RPM were output (processed files)Genome_build: Genome Reference Consortium mouse genome (GRCm39.p6)Supplementary_files_format_and_content: tab-delimited text files include reads or log2 RPM for each sample showing all genes or differential expression between conditions.